SDM report

Author

Claire

Published

2024-09-17

1 Dataset

The models are based on trawling data on the west coast

There are three data sources; IBTS, BITS and NATS

2 Trawl surveys

Information about the trawl surveys…

3 Catches

4 Predictors

  Variables      VIF
1     bTemp 4.043284
2      bSal 2.161882
3     Depth 3.196960
4    botCur 1.307152
5     slope 1.190949
6   fishInt 1.382509
7      maxT 3.904484

5 Presence / Absence models (Biomod2)


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Modeling folder : C:/Github_projects/SDM_Claire/model output/20240917/PA

Species modeled : Plaice

Modeling id : Plaice_2005_2022_AllYear

Considered variables : bTemp bSal Depth botCur slope fishInt maxT


Computed Models :  Plaice_allData_RUN1_GLM Plaice_allData_RUN1_GBM 
Plaice_allData_RUN1_RF Plaice_allData_RUN1_XGBOOST Plaice_allData_RUN2_GLM 
Plaice_allData_RUN2_GBM Plaice_allData_RUN2_RF Plaice_allData_RUN2_XGBOOST 
Plaice_allData_allRun_GLM Plaice_allData_allRun_GBM Plaice_allData_allRun_RF 
Plaice_allData_allRun_XGBOOST


Failed Models :  Plaice_allData_RUN1_GAM Plaice_allData_RUN2_GAM 
Plaice_allData_allRun_GAM

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.ensemble.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=

sp.name : Plaice

expl.var.names : bTemp bSal Depth botCur slope fishInt maxT


models computed: Plaice_EMwmeanByROC_mergedData_mergedRun_mergedAlgo

models failed: none

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Modeling folder : C:/Github_projects/SDM_Claire/model output/20240917/PA

Species modeled : Cod

Modeling id : Cod_2005_2022_AllYear

Considered variables : bTemp bSal Depth botCur slope fishInt maxT


Computed Models :  Cod_allData_RUN1_GLM Cod_allData_RUN1_GBM 
Cod_allData_RUN1_RF Cod_allData_RUN1_XGBOOST Cod_allData_RUN2_GLM 
Cod_allData_RUN2_GBM Cod_allData_RUN2_RF Cod_allData_RUN2_XGBOOST 
Cod_allData_allRun_GLM Cod_allData_allRun_GBM Cod_allData_allRun_RF 
Cod_allData_allRun_XGBOOST


Failed Models :  Cod_allData_RUN1_GAM Cod_allData_RUN2_GAM 
Cod_allData_allRun_GAM

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


-=-=-=-=-=-=-=-=-=-=-=-=-= BIOMOD.ensemble.models.out -=-=-=-=-=-=-=-=-=-=-=-=-=

sp.name : Cod

expl.var.names : bTemp bSal Depth botCur slope fishInt maxT


models computed: Cod_EMwmeanByROC_mergedData_mergedRun_mergedAlgo

models failed: none

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

6 Abundansmodell (SDM)

class                                 : sdmModels 
======================================================== 
number of species                     :  1 
number of modelling methods           :  3 
names of modelling methods            :  glm, brt, rf 
replicate.methods (data partitioning) :  subsampling 
number of replicates (each method)    :  2 
toral number of replicates per model  :  2 (per species) 
test percentage (in subsampling)      :  25 
------------------------------------------
model run success percentage (per species)  :
------------------------------------------
method          Plaice           
---------------------- 
glm        :        100   %
brt        :        100   %
rf         :        100   %

###################################################################
model Mean performance (per species), using test dataset (generated using partitioning):
-------------------------------------------------------------------------------

 ## species   :  Plaice 
=========================

methods    :     RMSE     |     COR     |     MAE     |     Deviance 
-------------------------------------------------------------------------
glm        :     1074.15 |     0.31    |     436.61  |     -865.19  
brt        :     1075.9  |     0.41    |     420.38  |     -898.91  
rf         :     1014.34 |     0.45    |     430.33  |     -703.06  
```  modelID species method replication replicationID success training test.dep
1       1  Plaice    glm subsampling             1    TRUE     TRUE     TRUE
2       2  Plaice    glm subsampling             2    TRUE     TRUE     TRUE
3       3  Plaice    brt subsampling             1    TRUE     TRUE     TRUE
4       4  Plaice    brt subsampling             2    TRUE     TRUE     TRUE
5       5  Plaice     rf subsampling             1    TRUE     TRUE     TRUE
6       6  Plaice     rf subsampling             2    TRUE     TRUE     TRUE
  test.indep
1      FALSE
2      FALSE
3      FALSE
4      FALSE
5      FALSE
6      FALSE

class                                 : sdmModels 
======================================================== 
number of species                     :  1 
number of modelling methods           :  3 
names of modelling methods            :  glm, brt, rf 
replicate.methods (data partitioning) :  subsampling 
number of replicates (each method)    :  2 
toral number of replicates per model  :  2 (per species) 
test percentage (in subsampling)      :  25 
------------------------------------------
model run success percentage (per species)  :
------------------------------------------
method          Cod              
---------------------- 
glm        :        100   %
brt        :        100   %
rf         :        100   %

###################################################################
model Mean performance (per species), using test dataset (generated using partitioning):
-------------------------------------------------------------------------------

 ## species   :  Cod 
=========================

methods    :     RMSE     |     COR     |     MAE     |     Deviance 
-------------------------------------------------------------------------
glm        :     764.86  |     0.35    |     392.6   |     -702.1   
brt        :     630.03  |     0.41    |     232.94  |     -487.34  
rf         :     785.83  |     0.41    |     343.93  |     -572.55  
```  modelID species method replication replicationID success training test.dep
1       1     Cod    glm subsampling             1    TRUE     TRUE     TRUE
2       2     Cod    glm subsampling             2    TRUE     TRUE     TRUE
3       3     Cod    brt subsampling             1    TRUE     TRUE     TRUE
4       4     Cod    brt subsampling             2    TRUE     TRUE     TRUE
5       5     Cod     rf subsampling             1    TRUE     TRUE     TRUE
6       6     Cod     rf subsampling             2    TRUE     TRUE     TRUE
  test.indep
1      FALSE
2      FALSE
3      FALSE
4      FALSE
5      FALSE
6      FALSE

7 Validering